MSFragger

Running MSstats using MSstats.csv from IonQuant

Using the .d folders (raw TIMS-TOF PASEF data) as input according to the FragPipe tutorial, IonQuant can generate a MSstats compatible file MSstats.csv.
Given an experimental setup that looks like this in the ‘Select LC/MS Files’ tab of FragPipe:

The MSstats.csv file output from IonQuant (via FragPipe) will look something like this:

This MSstats.csv file can be read by MSstats without any conversion. The R command for installing MSstats is:

With processedData, users can perform various downstream analyses described in the MSstats user manual.

Convert processedData into a protein intensity table (optional)

Although processedData generated by MSstats is suitable for data analysis in R, it is not reader-friendly. Here we provide a R script that converts this data structure into a protein intensity table after running MSstats: